BMRB: 34653

NMR structure of a peptide deriving from SARS-CoV-2 Lineages P.1 and B.1.351 S RBD 482-506 fragment in HFIP/H2O

Authors

Santoro, A., Buonocore, M., Grimaldi, M., D'Ursi, A.

Assembly

Spike glycoprotein

Entity

1. Spike glycoprotein (polymer), 25 monomers, 2821.123 Da Detail

GVKGFNCYFP LQSYGFQPTY GVGYQ

Formula weight

2821.123 Da

Source organism

Severe acute respiratory syndrome coronavirus 2

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chemcal Shifts

¹H: 153, ¹³C: 54 assignments Detail

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• TSV

ID	Entity ID	Seq ID	Comp ID	Atom ID	Atom type	Val	Val err	Ambig. code
1	1	1	GLY	HA2	H	3.817	0.022
2	1	1	GLY	HA3	H	3.817	0.022
3	1	1	GLY	CA	C	41.955	0.000
4	1	2	VAL	H	H	8.056	0.003
5	1	2	VAL	HA	H	4.076	0.005
6	1	2	VAL	HB	H	1.987	0.015
7	1	2	VAL	HG11	H	0.849	0.013
8	1	2	VAL	HG12	H	0.849	0.013
9	1	2	VAL	HG13	H	0.849	0.013
10	1	2	VAL	HG21	H	0.849	0.013
11	1	2	VAL	HG22	H	0.849	0.013
12	1	2	VAL	HG23	H	0.849	0.013
13	1	2	VAL	CA	C	61.440	0.000
14	1	2	VAL	CB	C	31.509	0.000
15	1	2	VAL	CG2	C	18.785	0.000
16	1	3	LYS	H	H	7.962	0.005
17	1	3	LYS	HA	H	4.249	0.013
18	1	3	LYS	HB2	H	1.775	0.005
19	1	3	LYS	HB3	H	1.689	0.006
20	1	3	LYS	HG2	H	1.380	0.023
21	1	3	LYS	HG3	H	1.353	0.007
22	1	3	LYS	HD2	H	1.624	0.002
23	1	3	LYS	HD3	H	1.624	0.002
24	1	3	LYS	HE2	H	2.905	0.013
25	1	3	LYS	HE3	H	2.905	0.013
26	1	3	LYS	CA	C	55.135	0.000
27	1	3	LYS	CB	C	31.519	0.021
28	1	3	LYS	CG	C	23.200	0.022
29	1	3	LYS	CD	C	27.586	0.000
30	1	3	LYS	CE	C	40.683	0.000
31	1	4	GLY	H	H	7.926	0.006
32	1	4	GLY	HA2	H	3.783	0.019
33	1	4	GLY	HA3	H	3.783	0.019
34	1	4	GLY	CA	C	43.705	0.000
35	1	5	PHE	H	H	7.657	0.008
36	1	5	PHE	HA	H	4.516	0.011
37	1	5	PHE	HB2	H	3.012	0.020
38	1	5	PHE	HB3	H	3.012	0.020
39	1	5	PHE	HD1	H	7.092	0.000
40	1	5	PHE	HD2	H	7.092	0.000
41	1	5	PHE	HE1	H	7.183	0.000
42	1	5	PHE	HE2	H	7.183	0.000
43	1	5	PHE	CA	C	56.487	0.000
44	1	5	PHE	CB	C	38.136	0.000
45	1	6	ASN	H	H	7.960	0.006
46	1	6	ASN	HA	H	4.518	0.010
47	1	6	ASN	HB2	H	2.614	0.003
48	1	6	ASN	HB3	H	2.614	0.003
49	1	6	ASN	CA	C	51.930	0.000
50	1	6	ASN	CB	C	37.100	0.000
51	1	7	CYS	H	H	7.669	0.005
52	1	7	CYS	HA	H	4.297	0.010
53	1	7	CYS	HB2	H	2.745	0.004
54	1	7	CYS	HB3	H	2.646	0.020
55	1	7	CYS	CA	C	57.066	0.000
56	1	7	CYS	CB	C	26.130	0.045
57	1	8	TYR	H	H	7.744	0.017
58	1	8	TYR	HA	H	4.508	0.007
59	1	8	TYR	HB2	H	2.967	0.013
60	1	8	TYR	HB3	H	2.790	0.017
61	1	8	TYR	HD1	H	5.990	0.999
62	1	8	TYR	HD2	H	5.990	0.999
63	1	8	TYR	HE1	H	6.964	0.013
64	1	8	TYR	HE2	H	6.964	0.013
65	1	8	TYR	CA	C	56.481	0.000
66	1	8	TYR	CB	C	37.227	0.045
67	1	9	PHE	H	H	8.018	0.001
68	1	9	PHE	HA	H	4.581	0.000
69	1	9	PHE	HB2	H	2.747	0.013
70	1	9	PHE	HB3	H	2.747	0.013
71	1	9	PHE	CB	C	37.213	0.000
72	1	10	PRO	HA	H	4.211	0.021
73	1	10	PRO	HB2	H	2.188	0.011
74	1	10	PRO	HB3	H	1.773	0.007
75	1	10	PRO	HG2	H	1.839	0.006
76	1	10	PRO	HG3	H	1.839	0.006
77	1	10	PRO	HD2	H	3.550	0.016
78	1	10	PRO	HD3	H	3.202	0.006
79	1	10	PRO	CA	C	62.952	0.000
80	1	10	PRO	CB	C	30.005	0.076
81	1	10	PRO	CG	C	25.737	0.000
82	1	10	PRO	CD	C	49.125	0.000
83	1	11	LEU	H	H	6.771	0.008
84	1	11	LEU	HA	H	4.143	0.009
85	1	11	LEU	HB2	H	1.536	0.014
86	1	11	LEU	HB3	H	1.536	0.014
87	1	11	LEU	HD11	H	0.842	0.008
88	1	11	LEU	HD12	H	0.842	0.008
89	1	11	LEU	HD13	H	0.842	0.008
90	1	11	LEU	HD21	H	0.766	0.004
91	1	11	LEU	HD22	H	0.766	0.004
92	1	11	LEU	HD23	H	0.766	0.004
93	1	11	LEU	CA	C	55.087	0.000
94	1	11	LEU	CB	C	40.389	0.000
95	1	11	LEU	CD1	C	22.437	0.000
96	1	11	LEU	CD2	C	21.001	0.000
97	1	12	GLN	H	H	7.973	0.006
98	1	12	GLN	HA	H	4.152	0.012
99	1	12	GLN	HB2	H	2.023	0.012
100	1	12	GLN	HB3	H	2.023	0.012
101	1	12	GLN	HG2	H	2.294	0.015
102	1	12	GLN	HG3	H	2.294	0.015
103	1	12	GLN	CA	C	55.769	0.000
104	1	12	GLN	CB	C	27.687	0.000
105	1	12	GLN	CG	C	32.463	0.000
106	1	13	SER	H	H	7.811	0.017
107	1	13	SER	HA	H	4.241	0.017
108	1	13	SER	HB2	H	3.789	0.014
109	1	13	SER	HB3	H	3.678	0.016
110	1	13	SER	CA	C	57.762	0.000
111	1	13	SER	CB	C	62.361	0.013
112	1	14	TYR	H	H	7.664	0.007
113	1	14	TYR	HA	H	4.394	0.004
114	1	14	TYR	HB2	H	2.950	0.020
115	1	14	TYR	HB3	H	2.950	0.020
116	1	14	TYR	HD1	H	6.704	0.000
117	1	14	TYR	HD2	H	6.704	0.000
118	1	14	TYR	HE1	H	6.975	0.000
119	1	14	TYR	HE2	H	6.975	0.000
120	1	14	TYR	CB	C	37.774	0.000
121	1	15	GLY	H	H	7.772	0.009
122	1	15	GLY	HA2	H	3.742	0.021
123	1	15	GLY	HA3	H	3.742	0.021
124	1	15	GLY	CA	C	41.776	0.000
125	1	16	PHE	H	H	7.497	0.008
126	1	16	PHE	HA	H	4.428	0.005
127	1	16	PHE	HB2	H	2.990	0.012
128	1	16	PHE	HB3	H	2.990	0.012
129	1	16	PHE	HD1	H	7.099	0.000
130	1	16	PHE	HD2	H	7.099	0.000
131	1	16	PHE	HE1	H	7.185	0.000
132	1	16	PHE	HE2	H	7.185	0.000
133	1	16	PHE	CB	C	38.083	0.000
134	1	17	GLN	H	H	7.485	0.004
135	1	17	GLN	HA	H	4.476	0.009
136	1	17	GLN	HB2	H	1.956	0.009
137	1	17	GLN	HB3	H	1.753	0.005
138	1	17	GLN	HG2	H	2.239	0.013
139	1	17	GLN	HG3	H	2.239	0.013
140	1	17	GLN	CB	C	27.913	0.026
141	1	17	GLN	CG	C	32.278	0.000
142	1	18	PRO	HA	H	4.242	0.017
143	1	18	PRO	HB2	H	2.126	0.010
144	1	18	PRO	HB3	H	1.816	0.010
145	1	18	PRO	HG2	H	1.906	0.001
146	1	18	PRO	HG3	H	1.906	0.001
147	1	18	PRO	HD3	H	3.475	0.007
148	1	18	PRO	CA	C	62.346	0.000
149	1	18	PRO	CB	C	30.019	0.020
150	1	18	PRO	CG	C	25.508	0.000
151	1	18	PRO	CD	C	48.892	0.000
152	1	19	THR	H	H	7.408	0.006
153	1	19	THR	HA	H	4.159	0.011
154	1	19	THR	HB	H	4.109	0.026
155	1	19	THR	HG21	H	1.051	0.012
156	1	19	THR	HG22	H	1.051	0.012
157	1	19	THR	HG23	H	1.051	0.012
158	1	19	THR	CA	C	60.288	0.000
159	1	19	THR	CB	C	68.240	0.000
160	1	19	THR	CG2	C	19.413	0.000
161	1	20	TYR	H	H	7.604	0.004
162	1	20	TYR	HA	H	4.384	0.007
163	1	20	TYR	HB2	H	2.967	0.005
164	1	20	TYR	HB3	H	2.897	0.011
165	1	20	TYR	HD1	H	6.701	0.001
166	1	20	TYR	HD2	H	6.701	0.001
167	1	20	TYR	HE1	H	6.970	0.007
168	1	20	TYR	HE2	H	6.970	0.007
169	1	20	TYR	CB	C	37.160	0.001
170	1	21	GLY	H	H	7.774	0.001
171	1	21	GLY	HA2	H	3.860	0.003
172	1	21	GLY	HA3	H	3.860	0.003
173	1	21	GLY	CA	C	43.661	0.000
174	1	22	VAL	H	H	7.472	0.004
175	1	22	VAL	HA	H	3.964	0.012
176	1	22	VAL	HB	H	2.005	0.009
177	1	22	VAL	HG11	H	0.849	0.015
178	1	22	VAL	HG12	H	0.849	0.015
179	1	22	VAL	HG13	H	0.849	0.015
180	1	22	VAL	HG21	H	0.849	0.015
181	1	22	VAL	HG22	H	0.849	0.015
182	1	22	VAL	HG23	H	0.849	0.015
183	1	22	VAL	CA	C	61.659	0.000
184	1	22	VAL	CB	C	31.073	0.000
185	1	22	VAL	CG2	C	18.377	0.000
186	1	23	GLY	H	H	7.931	0.002
187	1	23	GLY	HA2	H	3.891	0.024
188	1	23	GLY	HA3	H	3.713	0.005
189	1	23	GLY	CA	C	43.710	0.045
190	1	24	TYR	H	H	7.511	0.009
191	1	24	TYR	HA	H	4.498	0.017
192	1	24	TYR	HB2	H	2.891	0.007
193	1	24	TYR	HB3	H	2.891	0.007
194	1	24	TYR	HD1	H	6.708	0.000
195	1	24	TYR	HD2	H	6.708	0.000
196	1	24	TYR	HE1	H	6.954	0.000
197	1	24	TYR	HE2	H	6.954	0.000
198	1	24	TYR	CB	C	37.184	0.000
199	1	25	GLN	H	H	7.696	0.016
200	1	25	GLN	HA	H	4.242	0.010
201	1	25	GLN	HB2	H	2.063	0.010
202	1	25	GLN	HB3	H	1.880	0.009
203	1	25	GLN	HG2	H	2.217	0.019
204	1	25	GLN	HG3	H	2.217	0.019
205	1	25	GLN	CA	C	53.784	0.000
206	1	25	GLN	CB	C	27.941	0.074
207	1	25	GLN	CG	C	31.953	0.000

Release date

2021-08-29

Citation

Structural analysis of a simplified model reproducing SARS-CoV-2 S RBD/ACE2 binding site
Buonocore, M., Santoro, A., Grimaldi, M., Covelli, V., Firoznezhad, M., Rodriquez, M., Santin, M., D'Ursi, A.M.
Heliyon (2022), 8, e11568-e11568, PubMed 36406731 , DOI 10.1016/j.heliyon.2022.e11568 , Abstract

Related entities 1. Spike glycoprotein, : 1 : 99 : 1 entities Detail

Experiments performed 3 experiments Detail